Hi, Thank you for your reply.
My concern is that if rcoulomb and rvdw are set to be zero, does it mean that there are no coulombic and van der waals forces involved in the simulation? I guess there are still coulombic and van der waals forces between atoms of a single protein molecule. Or does setting the cutoff to be zero just mean there is no forces between neighbored molecules? Thanks. Huilin ________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of David van der Spoel [sp...@xray.bmc.uu.se] Sent: Wednesday, November 30, 2011 3:00 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gas-phase protein simulation yes all cutoffs 0 and epsilon_rf 1 and nstlist 0 as well. Toodle pip! On Nov 30, 2011, at 8:39 PM, "Shi, Huilin" <huil...@imail.iu.edu<mailto:huil...@imail.iu.edu>> wrote: Hi, I would like to run a gas-phase protein simulation (with charge state of +8). I have read this paper : Biochemistry, 2007, 47, 933-945. In the method section of vaccum simulation, it is said "For the remaining parameters, the same settings were used as in the water simulations, except that the periodic boundary conditions were turned off and no cutoffs whatsoever were used." I am confused about "no cutoffs whatsoever were used". Does that mean setting all the cutoffs to be zero? In the md.mdp file, can I use the following "; NEIGHBORSEARCHING PARAMETERS nstlist = 0 ns-type = simple pbc = no rlist = 0 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = cut-off rcoulomb = 0 epsilon_rf = 78 epsilon_r = 1 vdw-type = Cut-off rvdw = 0" Do I need to set rcoulomb/rvdw to zero or some other number? Thank you. Huilin -- gmx-users mailing list gmx-users@gromacs.org<mailto:gmx-users@gromacs.org> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org<mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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